Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid and AdoHcy (SAH)

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Cell-Effective Transition-State Analogue of Phenylethanolamine N -Methyltransferase.

Mahmoodi, N.Minnow, Y.V.T.Harijan, R.K.Bedard, G.T.Schramm, V.L.

(2023) Biochemistry 62: 2257-2268

  • DOI: https://doi.org/10.1021/acs.biochem.3c00103
  • Primary Citation of Related Structures:  
    7TWU, 7TX2

  • PubMed Abstract: 

    Phenylethanolamine N -methyltransferase (PNMT) catalyzes the S -adenosyl-l-methionine (SAM)-dependent methylation of norepinephrine to form epinephrine. Epinephrine is implicated in the regulation of blood pressure, respiration, Alzheimer's disease, and post-traumatic stress disorder (PTSD). Transition-state (TS) analogues bind their target enzymes orders of magnitude more tightly than their substrates. A synthetic strategy for first-generation TS analogues of human PNMT (hPNMT) permitted structural analysis of hPNMT and revealed potential for second-generation inhibitors [Mahmoodi, N.; J. Am. Chem. Soc. 2020, 142, 14222-14233]. A second-generation TS analogue inhibitor of PNMT was designed, synthesized, and characterized to yield a K i value of 1.2 nM. PNMT isothermal titration calorimetry (ITC) measurements of inhibitor 4 indicated a negative cooperative binding mechanism driven by large favorable entropic contributions and smaller enthalpic contributions. Cell-based assays with HEK293T cells expressing PNMT revealed a cell permeable, intracellular PNMT inhibitor with an IC 50 value of 81 nM. Structural analysis demonstrated inhibitor 4 filling catalytic site regions to recapitulate both norepinephrine and SAM interactions. Conformation of the second-generation inhibitor in the catalytic site of PNMT improves contacts relative to those from the first-generation inhibitors. Inhibitor 4 demonstrates up to 51,000-fold specificity for PNMT relative to DNA and protein methyltransferases. Inhibitor 4 also exhibits a 12,000-fold specificity for PNMT over the α 2 -adrenoceptor.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylethanolamine N-methyltransferase
A, B
294Homo sapiensMutation(s): 0 
Gene Names: PNMTPENT
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens)
Explore P11086 
Go to UniProtKB:  P11086
GTEx:  ENSG00000141744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11086
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KNX (Subject of Investigation/LOI)
Query on KNX

Download Ideal Coordinates CCD File 
N [auth B]5'-([(3S)-3-amino-3-carboxypropyl]{4-[(4R)-7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl]butyl}amino)-5'-deoxyadenosine
C27 H36 Cl2 N8 O5
Query on SAH

Download Ideal Coordinates CCD File 
C14 H20 N6 O5 S
Query on CD

Download Ideal Coordinates CCD File 
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.754α = 90
b = 93.754β = 90
c = 188.203γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Refinement description